We are working on leveraging the FHIR Connector Extension (3.6) that was recently released and trying to understand how can we separate out the different resources and respective request that come in a bundle to any other channel or do we have defined approach to handle bundle resource in extension.

What is "bundle resource in extension"? In particular resources of type Bundle do not have extensions at the root element.
What is "FHIR Extension", there are hundreds of them defined only by HL7, not talking about local ones.